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CAS No. : | 958-09-8 | MDL No. : | MFCD00005754 |
Formula : | C10H13N5O3 | Boiling Point : | - |
Linear Structure Formula : | - | InChI Key : | OLXZPDWKRNYJJZ-RRKCRQDMSA-N |
M.W : | 251.24 | Pubchem ID : | 13730 |
Synonyms : |
|
Chemical Name : | (2R,3S,5R)-5-(6-Amino-9H-purin-9-yl)-2-(hydroxymethyl)tetrahydrofuran-3-ol |
Num. heavy atoms : | 18 |
Num. arom. heavy atoms : | 9 |
Fraction Csp3 : | 0.5 |
Num. rotatable bonds : | 2 |
Num. H-bond acceptors : | 6.0 |
Num. H-bond donors : | 3.0 |
Molar Refractivity : | 61.51 |
TPSA : | 119.31 Ų |
GI absorption : | High |
BBB permeant : | No |
P-gp substrate : | No |
CYP1A2 inhibitor : | No |
CYP2C19 inhibitor : | No |
CYP2C9 inhibitor : | No |
CYP2D6 inhibitor : | No |
CYP3A4 inhibitor : | No |
Log Kp (skin permeation) : | -8.22 cm/s |
Log Po/w (iLOGP) : | 1.03 |
Log Po/w (XLOGP3) : | -0.55 |
Log Po/w (WLOGP) : | -1.27 |
Log Po/w (MLOGP) : | -1.54 |
Log Po/w (SILICOS-IT) : | -1.48 |
Consensus Log Po/w : | -0.76 |
Lipinski : | 0.0 |
Ghose : | None |
Veber : | 0.0 |
Egan : | 0.0 |
Muegge : | 0.0 |
Bioavailability Score : | 0.55 |
Log S (ESOL) : | -1.29 |
Solubility : | 12.9 mg/ml ; 0.0514 mol/l |
Class : | Very soluble |
Log S (Ali) : | -1.49 |
Solubility : | 8.21 mg/ml ; 0.0327 mol/l |
Class : | Very soluble |
Log S (SILICOS-IT) : | -0.4 |
Solubility : | 100.0 mg/ml ; 0.398 mol/l |
Class : | Soluble |
PAINS : | 0.0 alert |
Brenk : | 0.0 alert |
Leadlikeness : | 0.0 |
Synthetic accessibility : | 3.6 |
Signal Word: | Danger | Class: | 6.1 |
Precautionary Statements: | P301+P310 | UN#: | 2811 |
Hazard Statements: | H301 | Packing Group: | Ⅲ |
GHS Pictogram: |
* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
78% | With ammonia In methanol at 100℃; for 12h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
90% | With tetrabutyl ammonium fluoride In tetrahydrofuran | |
78% | With tetrabutyl ammonium fluoride In tetrahydrofuran at 75℃; for 1h; | |
With tetrabutyl ammonium fluoride Yield given; |
With tetrabutyl ammonium fluoride In tetrahydrofuran at 70℃; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With 1,1,1,3,3,3-hexamethyl-disilazane | ||
With 2,6-dimethylpyridine In N,N-dimethyl-formamide for 1h; Ambient temperature; | ||
With pyridine for 0.25h; |
With pyridine at 20℃; | ||
With pyridine for 0.5h; Ambient temperature; | ||
In pyridine 0 deg C then warmed to r.t. for 1-2 h; | ||
With triethylamine In pyridine | ||
With pyridine Ambient temperature; | ||
With pyridine | ||
In pyridine Ambient temperature; | ||
With pyridine for 0.5h; | ||
With pyridine at 0℃; for 0.5h; | ||
With pyridine | ||
With pyridine at 20℃; for 0.333333h; | ||
With pyridine at 20℃; for 0.5h; | ||
With pyridine In water at 20℃; for 2h; | Synthesis of N6-Dimethoxytrityl-2'-deoxyadenosine 2'-Deoxynucleoside (10 mmol) was coevaporated three times with pyridine and dried in vacuo for 12 h. Anhydrous pyridine (50 mL) and chlorotrimethylsilane (50 mmol) were added. After the mixture had been stirred at room temperature for 2 h, dimethoxytrityl chloride (3.7 g, 11 mmol) was added. The reaction was stirred overnight (~16 h) at room temperature. Water (60 mL) and aqueous ammonium hydroxide (2 mL, 28-30%) were added and the reaction mixture was stirred for 30 min. The crude product was extracted into dichloromethane The organic layer was washed two times with a 5% aqueous solution of sodium bicarbonate and dried with anhydrous sodium sulfate. The organic layer containing product was filtered from salts and purified by column chromatography using chloroform/pyridine (99.9:0.1) and a gradient of methanol (0-6%). Yield 99%. 1H NMR (DMSO-d6) δ 8.42 (s, 1H), 8.32 (s, 1H), 7.28-7.26 (m, 5H), 7.19 (d, 4H), 6.84 (d, 4H), 6.32 (t, 1H), 5.31 (d, 1H), 5.12 (t, 1H), 3.86-3.84 (m, 1H), 3.71 (s, 6H), 3.61-3.47 (m, 2H), 2,79-2.74 (m, 1H), 2.27-2.22 (m, 1H); 13C NMR (DMSO-d6) δ 157.69, 153.68, 151.16, 148.07, 145.34, 140.37, 137.27, 129.77, 128.39, 127.71, 126.47, 121.05, 113.00, 88.04, 84.12, 70.92, 69.61, 61.83, 54.99; HRMS (FAB) calcd for C31H31N5O5 (M+) 553.2325 found 553.2309. | |
With pyridine at 20℃; for 2h; | ||
With pyridine at 20℃; for 3.75h; Cooling with ice; | ||
With pyridine In dichloromethane at 0 - 20℃; for 18h; | GP I: N-butanoylation of nucleosides via transient TMS-protection: General procedure: The respective nucleoside (adenosine, guanosine, or 20-deoxyadenosine) was co-evaporatedthree times and then dissolved in anhydrous pyridine (2±5 mL/mmol), and diluted either with thesame volume of THF or double the volume of CH2Cl2. At 0 °C, TMSCl (2.1-9.0 equiv.) was added.The reaction mixture was allowed to warm up to rt and stirred for 5-18 h. Successively, butyrylchloride (1.1 equiv.) was added slowly and the reaction mixture stirred for another 6 h at rt. Cleavageof TMS ethers was promoted by the addition of either 1 M HCl (0.5 mL/mmol) under vigorous stirringfor 5 min, or methanol (2-5 mL/mmol) and stirring at rt for further 12 h. The reaction was terminatedby removal of all volatile components under high vacuum. The crude residue was co-evaporated withtoluene and CH2Cl2 several times, and then taken up in acetonitrile/demin. water. Purification was performed by means of automated RP flash column chromatography on C18 modified silica gel withan acetonitrile gradient in water (0% to 100%). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
80% | With subtilisin 8350 In N,N-dimethyl-formamide at 45℃; for 48h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
98% | With pyridine at 20℃; for 12h; | |
98% | With 1H-imidazole; dmap In N,N-dimethyl-formamide at 20℃; | |
96% | With pyridine Ambient temperature; |
96% | With pyridine for 2h; | |
92% | With pyridine at 20℃; | |
82% | ||
81% | With pyridine Reflux; | |
66% | With pyridine at 20℃; for 4h; Inert atmosphere; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
86% | With 1H-imidazole; methanesulfonic acid; N-ethyl-N,N-diisopropylamine In N,N-dimethyl-formamide at 20℃; for 2h; | |
77% | With pyridine; dmap; triethylamine for 4h; | |
68% | With pyridine at 0 - 20℃; |
With pyridine; dmap; triethylamine at 13℃; for 12h; | ||
Stage #1: 4,4'-dimethoxytrityl chloride; 2'-deoxy-D-adenosine With pyridine; dmap; triethylamine at 20℃; Stage #2: With methanesulfonyl chloride; triethylamine at 20℃; for 2h; | 4.D1 Step D1: 2.2 ml of Et3N and 175 mg of DMAP and then 5.25 g of DMTCl are added, at ambient temperature overnight, to 5 g of 2′-deoxyadenine dissolved in pyridine. 2.4 ml of Et3N and 1.27 ml of MsCl are then added to the mixture. After incubation for 2 h at ambient temperature, the mixture is filtered and washed with ethyl acetate. The filtrate is concentrated and dissolved in 75 ml of ethanol, to which is added 1M of NaOH. After refluxing for 1.5 h, the mixture is cooled to ambient temperature and 1M of HCl is added. The ethanol is evaporated off in a rotary evaporator and the residue is extracted with CH2Cl2. After silica gel column purification, the product dATP-D1 is obtained. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
99% | With chloro-trimethyl-silane In pyridine at 20℃; for 16h; | |
99% | Stage #1: 2'-deoxy-D-adenosine With pyridine; chloro-trimethyl-silane at 20℃; for 2h; Stage #2: 4,4'-dimethoxytrityl chloride With pyridine at 20℃; for 16h; | |
With chloro-trimethyl-silane Yield given. Multistep reaction; |
With chloro-trimethyl-silane; ammonia 1.) pyridine, 15 min, 2.) pyridine, 18 h, room t., 3.) dioxane, water, 2 days; Yield given. Multistep reaction; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
100% | With pyridine; dmap for 4h; Ambient temperature; | |
90% | With dmap; triethylamine In acetonitrile for 3h; | |
85% | With pyridine |
85% | With pyridine at 20℃; for 2h; | |
79% | With pyridine In dichloromethane at 20℃; for 1.5h; Cooling with ice; | Synthesis of 3′,5′-di-O-acetyl-2′-deoxyadenosine (b) To the solution of 2′-deoxyadenosine a (3 g, 11.95 mmol)in 40 mL of anhydrous pyridine 12 mL of acetic anhydride(119.5 mmol) were slowly dropped and the reactionmixture was stirred for 1.5 h at room temperature.Then, after cooling in the ice bath, 10 mL of CH2Cl2were added and the solution was washed with 10 % aq.NaHCO3 (50 mL). The aqueous layer was extracted twicewith 30 mL of chloroform. The combined organic layerswere dried with MgSO4, the drying agent was filtered offand chloroform evaporated under reduced pressure. Theresulting precipitate was three times evaporated with toluene(3 × 15 mL) and purified by crystallization fromethanol to give 3.18 g (9.5 mmol) of acetylated 2′-deoxyadenosineb (yield 79 %), TLC: Rf = 0.66, (CHCl3/MeOH 80:20 v/v). 1H NMR (250 MHz, CDCl3) δ 2.09(s, 3H, CH3COO), 2.14 (s, 3H, CH3COO), 2.62 (ddd,1H, JH2′,H3 = 2.5 Hz, JH2′,H1′ = 5.9 Hz, Jgem = 14.1 Hz,H2′), 2.96 (ddd, 1H, JH2″,H3′ = 6.3 Hz, JH2″,H1′ = 8.1 Hz,Jgem = 14.1 Hz, H2″), 4.32-4.46 (m, 3H, H4′, H5′,H5″), 5.43 (dt, 1H, JH3′,H2′ = JH3′,H4′ = 2.5 Hz,JH3′,H2″ = 6.3 Hz, H3′) 5.85 (bs, 2H, NH-6), 6.46 (dd, JH3′,H2″ = 6.3 Hz, H3′) 5.85 (bs, 2H, NH-6), 6.46 (dd,1H, JH1′,H2′ = 5.9 Hz, JH1′,H2″ = 8.1 Hz, H1), 7.99 (s, 1H,H2), 8.36 (s, 1H, H8). |
75% | In pyridine | |
74% | With pyridine 1.) 0 deg C, 1 h, 2.) 25 deg C, 5 h; | |
Stage #1: acetic anhydride; 2'-deoxy-D-adenosine With pyridine Heating; Stage #2: In methanol at 105℃; for 1.5h; | ||
With pyridine; dmap for 4h; | ||
With pyridine | ||
With dmap; trimethylamine In acetonitrile for 8h; Reflux; | 148 First step, a mixture of 2-deoxy-adenosine(3.6 g), acetic anhydride (5.47 g), trimethyl (4.07 g) and DMAP (0.16 g) in anhydrous acetonitrile (40 ml) was refluxed for 8 h. Acetonitrile was removed under reduced pressure. H2O (40 ml) was added to the residue, and the resulting solution was extracted with EtOAc (3 × 40 ml). The EtOAc of the combined organic layer was dried with sodium acetate and The EtOAc layer was filtered and the filtrate was concentrated. The residue was separated by column chromatography over silica gel and eluted with CHCl3-CH3OH (100 : 1) to yield 3',5'-diacetyl-2'-deoxy-adenosine (4.0 g). Second step, a mixture of 3', 5'- diacetyl-2'-deoxy-adenosine(1.2 g), tert-butyl nitrite (7.42 g), and tribromomethane (20 ml) was refluxed for 2 h. The excess tert-butyl nitrite was removed under reduced pressure. The residue was separated by column chromatography over silica gel and eluted with CHCl3-CH3OH (80 : 1) to yield 3',5'-diacetyl-2'-deoxy-6-bromo-adenosine (595 mg). Third step, a mixture of 3', 5'- diacetyl-2'-deoxy-6-bromo-adenosine (398 mg), 3-methoxy-4-hydroxybenzylamine (379.3 mg, the hydrochloride) and triethylamine (253 mg) in anhydrous EtOH (20 ml) was refluxed for 5 h. After evaporation, the residue was separated by column chromatography over silica gel and eluted with CHCl3-CH3OH (50 : 1) to yield N6-(3-methoxy-4-hydroxy-benzyl)-2-deoxy-3, 5'-diacetyl adenosine (340 mg): 1H NMR (300 MHz, acetone-d6):the 2-deoxy- adenosine moiety δ 8.29 (1H, s, H-8), 8.16 (1H, s, H-2), 7.33 (1H, t, J= 6.0 Hz, NH), 6.44 (1H, dd, J= 7.8, 6.3 Hz, H-1), 5.48 (1H, m, H-3'), 4.36 (1H, dd, J= 6.3, 12.9 Hz, H-5'a), 4.30 (1H, dd, J= 6.0, 12.9 Hz, H-5'b), 4.29 (1H, m, H-4'), 3.21 (1H, ddd, J= 7.5, 7.8, 15.0 Hz, H-2'a), 2.59 (1H, ddd, J = 2.4, 6.0, 15.0, H-2'b); the 3-methoxy-4-hydroxybenzyl moiety δ 7.63 (1H, brs, OH), 7.05 (1H, d, J= 1.5 Hz, H-2"), 6.87 (1H, dd, J= 7.8, 1.5 Hz, H-6"), 6.74 (1H, d, J= 7.8 Hz, H-5"), 4.76 (2H, brs, H-7"), 3.75 (3H, s, OMe); the acetyl δ2.09 (3H, s, CH3CO), 2.01 (3H, s, CH3CO); 13C NMR (300 MHz, acetone-d6):the 2-deoxy- adenosine moiety δ 155.9 (C-6), 153.6 (C-2), 149.1 (C-4), 139.9 (C-8), 121.2 (C-5), 85.2 (C-1), 83.1 (C-4'), 75.6 (C-3'), 64.5 (C-5'), 37.0 (C-2'); the 3-methoxy-4-hydroxy moiety δ 148.2 (C-3"), 146.5 (C-4"), 132.0 (C-1), 121.2 (C-2"), 115.6 (C-6"), 112.3 (C-5"), 56.1 (OMe), 44.2 (C-7"); the acetyl δ170.8, 170.7, 20.9, 20.6ο | |
4.0 g | With dmap In acetonitrile for 8h; Reflux; | 148 First step, a mixture of 2'-deoxy-adenosine (3.6 g), acetic anhydride (5.47 g), trimethyl (4.07 g) and DMAP (0.16 g) in anhydrous acetonitrile (40 ml) was refluxed for 8 h. Acetonitrile was removed under reduced pressure. H2O (40 ml) was added to the residue, and the resulting solution was extracted with EtOAc (3*40 ml). The EtOAc of the combined organic layer was dried with sodium acetate and The EtOAc layer was filtered and the filtrate was concentrated. The residue was separated by column chromatography over silica gel and eluted with CHCl3-CH3OH (100:1) to yield 3',5'-diacetyl-2'-deoxy-adenosine (4.0 g). |
With pyridine; dmap at 20℃; for 4h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With sodium hydrogencarbonate; In pyridine; methanol; chloroform; | A. Synthesis of N-benzoyl deoxyadenosine (hereinafter referred to as "dbzA") 50 mmol of deoxyadenosine (hereinafter referred to as "dA") is suspended in 150 ml of dry pyridine. 300 mmol of benzoylchloride is added dropwise while ice-cooling and then, the reaction mixture is warmed to room temperature, followed by stirring for about one hour. The completion of the reaction is confirmed by means of thin-layer chromatography (eluent: a 10:1 by volume mixture of chloroform and methanol). The reaction mixture is then poured into a mixture of 500 ml of chloroform, 350 g of ice and 28 g of sodium hydrogencarbonate. The resulting mixture is shaken in a separatory funnel, allowed to stand, and then the chloroform phase is taken out. The aqueous phase is extracted with two portions of chloroform, and the chloroform phase is taken out. The chloroform phases obtained are mixed together and washed with two portions of water. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
99% | With 1H-imidazole In N,N-dimethyl-formamide at 20℃; | |
98% | With 1H-imidazole In N,N-dimethyl-formamide for 15h; | |
96% | With 1H-imidazole In N,N-dimethyl-formamide at 35℃; for 16h; |
95% | With 1H-imidazole In N,N-dimethyl-formamide at 20℃; | |
95% | With triethylamine In N,N-dimethyl-formamide at 20℃; for 8h; Inert atmosphere; | |
95% | With 1H-imidazole In N,N-dimethyl-formamide at 20℃; for 14h; | Synthesis of 3',5'-O-bis(TBS)-2'-deoxyadenosine [11] Synthesis was performed according to the method described in the literature, using 2'-deoxyadenosine (10) as a starting material. 1H NMR spectrum was consistent with the literature value. |
92% | With 1H-imidazole In N,N-dimethyl-formamide at 60℃; for 1h; | |
87.3% | With pyridine; 1H-imidazole at 20℃; for 24h; Inert atmosphere; | |
84% | With 1H-imidazole; dmap In N,N-dimethyl-formamide for 0.5h; | |
84% | With 1H-imidazole In N,N-dimethyl-formamide at 0℃; for 0.5h; | 42.a To a solution of 2-deoxyadenosine (3.00 g, 11.1 mmol, 1.0 equiv) in DMF (16 mL) at 0° C. were added imidazole (4.54 g, 66.8 mmol, 6.0 equiv) and DMAP (200 mg, 1.6 mmol, 0.15 equiv). Next, a solution of TBSCI (4.20 g, 27.9 mmol, 2.5 equiv) in DMF (8.0 mL) was added dropwise at 0° C. and the reaction stirred 30 minutes. The reaction mixture was diluted with saturated aqueous NaHCO3 (100 mL) and extracted with EtOAc (3×100 mL). The combined organic extracts were dried (Na2SO4), filtered and concentrated under reduced pressure. Purification by flash chromatography (6:1 EtOAc/hexanes) afforded the title compound (4.5 g, 84%) as a white solid: mp 123-125° C.; Rf 0.7 (1:3 EtOAc/hexanes); [α]20D -2.7 (c 0.96, CHCl3); 1H NMR (600 MHz, CDCl3) δ 0.00 (s, 6H), 0.01 (s, 6H), 0.82 (s, 18H), 2.34 (ddd, J=13.2, 6.0, 4.2 Hz, 1H), 2.50-2.58 (m, 1H), 3.68 (dd, J=10.8, 3.0 Hz, 1H), 3.78 (dd, J=11.4, 4.2 Hz, 1H), 3.92 (dd, J=6.6, 3.0 Hz, 1H), 4.52 (dd, J=9.0, 3.6 Hz, 1H), 5.70 (br s, 2H), 6.36 (t, J=6.6 Hz, 1H), 8.05 (s, 1H), 8.26 (s, 1H); 13C NMR (150 MHz, CDCl3) δ -5.5, -5.4, -4.1, -4.7, 18.0, 18.4, 25.8, 26.0, 41.3, 62.8, 71.9, 84.3, 87.9, 120.0, 139.1, 149.6, 152.8, 155.3; HRMS (ESI+) calcd for C22H40N5O3Si2 [M-H]+ 478.2664, found 478.2656 (error 1.7 ppm). |
80% | With 1H-imidazole; dmap In N,N-dimethyl-formamide at 20℃; Inert atmosphere; | 1 1.2 tert-butyldimethylsilyl chloride (TBDMSCI, 2.5 mmol) was added to a solution of dry nucleoside (1.0 mmol), dimethyl aminopridine (DMAP, 0.15 mmol) and imidazole (6 mmol) in anhydrous DMF (10 mL). After the reaction mixture was stirred overnight at room temperature under nitrogen, it was quenched with sat. aq. NaHCO3, and extracted with dichloromethane. The combined organic layer was concentrated, and the residue was purified by silica gel flash chromatography with a gradient eluent of CH2Cl2-CH3OH from 100:0 to 100:5. 3',5'-Bis-O-(tert-butyldimethylsilyl)-deoxyadenosine (1): yield 80%. 1H NMR (500 MHz, CDCl3): δ 8.29 (s, 1H, 2-H), 8.09 (s, 1H, 8-H), 6.65 (br s, 2H, NH2), 6.41 (t, 1H, 1'-H), 4.56 (dd, 1H, 3'-H), 3.96 (d, 1H, 4'-H), 3.82 (dd, 1H, 5'-H), 3.72 (dd, 1H, 5"-H), 2.59 (m, 1H, 2'-H), 2.39 (m, 1H, 2"-H), 0.86 (s, 18H, (CH3)3CSi), 0.05 (s, 6H, CH3SiO), 0.03 (s, 6H, CH3SiO). HRMS (APCI): calcd for C22H41N5O3Si2+H, -480.2826. found, 480.2818. |
78% | With 1H-imidazole In N,N-dimethyl-formamide | |
73% | With triethylamine In N,N-dimethyl-formamide at 20℃; for 3h; | |
58% | With pyridine; dmap; 4 A molecular sieve for 72h; | |
With 1H-imidazole; acetic acid 1.) pyridine, room temperature, 2 d, 2.) room temperature, 30 min; Yield given. Multistep reaction; | ||
With 1H-imidazole In N,N-dimethyl-formamide | ||
With 1H-imidazole In N,N-dimethyl-formamide | ||
Stage #1: 2'-deoxy-D-adenosine With 1H-imidazole In N,N-dimethyl-formamide for 0.25h; Cooling with ice; Stage #2: tert-butyldimethylsilyl chloride In tetrahydrofuran; N,N-dimethyl-formamide at 20℃; for 24.0833h; | 2.1 An anhydrous mixture of dA (10, 10 g), imidazole (4.1 g), and DMF (150 mL) was placed under a dry atmosphere and cooled in an ice/water bath for 15 minutes. A solution of TBDMS-C1 (9 g) in anhydrous THF (25 mL) was added over 5 minutes. The resulting mixture was stirred at room temperature for 24 hours. The solution was concentrated in vacuo and the residual syrup was partitioned between EtOAc (300 mL), Hexane (30 mL), and water (300 mL). The layers were separated, and the organic layer was washed with 10% aqueous sodium bicarbonate (2 X 300 mL), dried over dried over anhydrous sodium sulfate, filtered, and concentrated at reduced pressure. The solid was triturated with hexanes, filtered, and dried in vacuo to afford 11a. TLC (silica gel on glass, 50EtOAc:50DCM) shows a single spot, Rf = 0.30. | |
With 1H-imidazole In N,N-dimethyl-formamide | 5 The synthesis of 27 commences with commercially available deoxyadenosine 22 which is silylated at both hydroxyl groups furnishing 23. The NPOM caging group is installed on N-6 using NaH as the base in DMF. Converting N-6 into a secondary amine (as in 24) has been shown to be sufficient as a protecting strategy for chemical DNA synthesis. The TBDMS groups is subsequently removed by treatment with NH4F and the 5'-OH in 25 is selectively blocked by DMT protection leading to 26. The synthesis of 27 is completed through phosphoramidite formation. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
85% | With 1H-imidazole In N,N-dimethyl-formamide at 0 - 20℃; | |
77% | With 1H-imidazole In N,N-dimethyl-formamide for 1.5h; | |
75% | With 1H-imidazole In N,N-dimethyl-formamide Ambient temperature; |
75% | With 1H-imidazole In N,N-dimethyl-formamide at 20℃; for 4h; | 40.a; 96.a Example 40: ((2R,3S,4R,5R)-5-{4-[(lS)-2,3-Dihydro4H-inden-l-ylamino]-7H-pyrrolo[2,3-2SO4 and concentrated in vacuo. The product was isolated as a white solid (4.138 g, 75 %) and was used without further purification.[0304] LCMS: R.t. 1.31 min, ES+ 366 (formic acid).; Example 96: [(2R,3S,5R)-3-hydroxy-5-(6-phenyl-9H-purin-9-yl)tetrahydrofuran-2-yl]- methyl sulfamate (1-93)Step a: (2R3S,5R)-5-(6-amino-9I-purin-9-yl)-2-({ rtert-butyl(dimethyl)silyl1oxy tmethyl)- tetrahydrofuran-3-ol[0709] To a solution of dry (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-2-(hydroxymethyl)tetrahydrofuran-3-ol (3.78 g, 15.04 mmol) and imidazole (2.46 g, 36.1 mmol) in DMF (20 mL) was added TBSCl (2.38 g, 15.80 mmol) and the solution was stirred at r.t. for 4 hours. The reaction mixture was diluted with water (100 mL), and extracted with EtOAc (3 x 100 mL). The combined organics were dried (Na2SO4)and concentrated. The product was isolated as a white solid (4.138 g, 75%) and was used without further purification.[0710] LCMS: R.t. 1.31 min ES+ 366 (formic acid) |
72% | With pyridine; 1H-imidazole In N,N-dimethyl-formamide at 20℃; | |
48% | In N,N-dimethyl-formamide at 25℃; for 12h; | 11.1 Step 1: preparation of compound 11b To a solution of compound ha (4.1 g, 16.383 mmol, 1.0 eq) in pyridine (50 mL) was added 4-dimethylaminopyridine (0.4 g, 3.277 mmol, 0.2 eq) and tert-butyldimethylsilylchloride (3.704 g, 24.575 mmol, 1.5 eq) at 25 °C. Then the reaction mixture was stirred at25 °C for 12 h. The solvent was concentrated under reduced pressure to give a residuethat was purified by column chromatography on silica gel (DCM/MeOH=50/1 to 10/1) toafford compound llb (2.86 g, 48 % yield) as a white solid. ‘H NIVIR (400 MHz, CD3OD)8.32 (s, 1H), 8.21 (s, 1H), 6.47 (dd, J=5.2, 7.2 Hz, 1H), 4.31 - 4.18 (m, 2H), 4.06 - 3.96(m, 1H), 3.94 - 3.84 (m, 1H), 3.18 - 3.06 (m, 1H), 2.80 - 2.70 (m, 1H), 0.85 (s, 9H), 0.03 (d, J9.6 Hz, 6H); ESI-MS m/z 365.1 [M+lfb. |
With pyridine cooling; | ||
With pyridine at 20℃; for 4h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
52% | With PS lipase In tetrahydrofuran at 30℃; | |
52% | With PSL lipase In tetrahydrofuran at 30℃; for 60h; Yields of byproduct given; | |
28% | With Pseudomonas fluorescence lipase In tetrahydrofuran at 30℃; for 36h; |
With Pseudomonas cepacia lipase In tetrahydrofuran at 30℃; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
78% | In tetrahydrofuran at 30℃; for 8h; lipase from C. antarctica; | |
75% | With CA lipase In tetrahydrofuran at 5℃; | |
With Candida antarctica lipase B In tetrahydrofuran at 45℃; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
65% | With pyridine at -5℃; | |
62% | With pyridine; dmap In dichloromethane at 0℃; for 3h; | |
37% | With pyridine at 0℃; |
18% | With pyridine at 0℃; for 96h; Inert atmosphere; | |
With pyridine at 0℃; for 16h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
91% | With pyridine | |
88% | With pyridine at 20℃; for 18h; Inert atmosphere; | |
84% | With pyridine; 1H-imidazole at 20℃; |
80% | With pyridine; dmap; triethylamine for 48h; Ambient temperature; | |
75% | With pyridine at 22 - 25℃; | |
72% | regioselective reaction; | |
63% | With pyridine; 1H-imidazole In N,N-dimethyl-formamide for 2h; | 16.1.1 . 1.1 Interemediate 16-i 2 '-Deoxy adenosine (15.0 g,58.5 mmol, 1.0 equiv.) and imidazole (9.96 g, 146 mmol, 2.5 equiv.) were dissolved in dry pyridine (100 mL) and concentrated in vacuo. The resulting mixture was dissolved in anhydrous DMF (75 mL), TBDPSC1 (16.3 mL, 61.4 mmol, 1.1 equiv.) was added, and the mixture was stirred for 2 h. The solution was concentrated in vacuo then dissolved in EtOAc (500 mL), and washed with water (2 x 250 mL), then brine (250 mL). The organic layer was dried over MgS04, filtered, and concentrated in vacuo to afford a thick oil that was purified by flash column (0920) chromatography over silica gel (0% to 5% MeOH in EtOAc) to afford the product as a white solid 16-i (18.0 g, 63%) spectral characteristics consistent with the literature (Krishnakumar, K., et ah, Synlett 7, 1055-1058 (2010)). |
12% | With 1H-imidazole In dichloromethane at 20℃; for 48h; Inert atmosphere; | 17E Example 17E: (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-2-(((tert-butyldiphenylsilyl)oxy)methyl)tetrahydrofuran-3-ol TBDPS-CI (1.8 mL, 7.06 mmol) was added dropwise over 40 minutes to a stirred suspension of 2-deoxyadenosine monohydrate (2.0 g, 7.43 mmol) and imidazole (1.52 g, 22.3 mmol) in DCM (100 mL) under a nitrogen atmosphere. The resulting white suspension was stirred at room temperature for 2 days. Water (50 mL) was added and the mixture extracted with DCM (3 x 100mL). The combined organic extracts were dried (Na2S04) and the solvent evaporated in vacuo to leave a colourless oil. This was purified by flash column chromatography using an increasing gradient from 50-100% EtOAc/hexane then 2-10% MeOH/EtOAc to give the product (430 mg, 0.88 mmol, 12%) as a white foam. UPLC-MS (Acidic 2 min): rt 1.00 min, m/z 490 [M+H]+H NMR (400 MHz, CDCI3) δ ppm: H NMR (400 MHz, CHLOROFORM-d) δ ppm 1.06 (s, 9 H) 2.49 - 2.57 (m, 1 H) 2.75 (dd, J^13.30, 6.65 Hz, 1 H) 3.82 - 3.95 (m, 2 H) 4.04 - 4.15 (m, 1 H) 4.71 - 4.75 (m, 1 H) 5.73 (br s, 2 H) 6.45 (t, J=6.46 Hz, 1 H) 7.11 (s, 1 H) 7.33 - 7.45 (m, 6 H) 7.60 - 7.66 (m, 4 H) 8.02 (s, 1 H) 8.29 (s, 1 H) |
With 1H-imidazole In pyridine at 20℃; for 5h; | ||
With pyridine for 24h; Ambient temperature; | ||
With pyridine at 20℃; | ||
With 1H-imidazole In N,N-dimethyl-formamide |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
100% | With 3-chloro-benzenecarboperoxoic acid In methanol Ambient temperature; | |
90% | With 3-chloro-benzenecarboperoxoic acid In methanol for 5h; Ambient temperature; | |
With 3-chloro-benzenecarboperoxoic acid In methanol at 30℃; for 7h; |
With 3-chloro-benzenecarboperoxoic acid In methanol; water for 16h; Ambient temperature; | ||
Multi-step reaction with 2 steps 1: 78 percent / 1.) dinitrophenoxyamine, 2.) aq. HCl / dimethylformamide / 24 h / 37 °C 2: 84 percent / hydroxylamine, aq. NaOH / 48 h / 50 °C |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
100% | With bromine; sodium acetate; acetic acid In water at 20 - 50℃; | |
88% | With bromine; sodium acetate | |
88% | With sodium azide; bromoisocyanuric acid monosodium salt In water; N,N-dimethyl-formamide at 20℃; for 0.5h; | General procedure: 5'-O-Monomethoxytrityl-N2-phenoxyacetylguanosine (33, 0.138 g, 0.2 mmol) was dissolved inaqueous DMF solution (H2O:DMF 1:4, 5 mL) under stirring. SMBI (1.1 equiv., 0.051 g, 0.22 mmol)was added at r.t. and the mixture stirred. Progress of the reaction was followed by TLC. An additionalamount of the reagent (0.15 equiv., 0.007 g) was added into the reaction mixture after 1.5 h. Oncompletion of the reaction by 2 h, the reaction mixture was filtered, evaporated to dryness underreduced pressure and coevaporated with water (2 × 2 mL). The crude reaction mixture was purified bycolumn chromatography (4%-5% MeOH in DCM, v/v) to afford nucleoside 34 (0.148 g, 96%) in pureform as a white solid.8-Bromo-5'-O-monomethoxytrityl-N2-phenoxyacetylguanosine (34). |
83% | With bromine at 20℃; for 16h; aq. acetate buffer; | |
82% | With bromine In acetate buffer at 20℃; | |
81% | With bromine; sodium acetate at 20℃; aq. acetate buffer; | |
81% | With bromine In aq. acetate buffer at 20℃; for 18h; | |
79% | With bromine In acetate buffer at 20℃; for 4h; | |
75.5% | With bromine In 1,4-dioxane at 20℃; | |
69% | With bromine In aq. acetate buffer at 20℃; for 3h; | |
68% | With 1,3-dibromo-5,5-dimethylimidazolidine-2,4-dione In N,N-dimethyl-formamide at 25℃; for 3.5h; | Typical procedure for the bromination of unprotected nucleosides: DBH (323 mg, 1.13 mmol) was added to a stirred solution of 1d (500 mg, 2.05 mmol) in DMF (5 mL). The resulting pale-yellow solution was stirred at room temperature for 20 minutes or until TLC showed absence of starting material and formation of less polar product. Volatiles were evaporated and the residue was coevaporated with MeCN. The resulting pale solid was crystallized from hot acetone to give 2d (500 mg, 75%) as colorless crystals with data as reported.14 |
67% | With bromine | |
61% | With bromoisocyanuric acid monosodium salt In water; N,N-dimethyl-formamide at 25℃; for 1.5h; Inert atmosphere; | |
40% | With N-Bromosuccinimide In N,N-dimethyl-formamide for 12h; Ambient temperature; | |
40% | With bromine; sodium acetate In water | |
34% | With bromine In water for 3h; | |
30.4% | With bromine In water at 20℃; for 24h; Heating; | |
25% | With N-Bromosuccinimide In methanol at 40℃; for 18h; | 8 Synthesis of Compound (16) (8-bromo-2'-deoxyadenosine) To a solution of deoxyadenosine (15) (3 g, 11 mmol) in methanol (50 ml) was added NBS (2.6 g, 14.6 mmol, 1.3 eq.). The mixture was stirred at 40° C. for 18 h. The pink suspension was filtered, and the filtrate was dried in vacuo to yield compound (16) (900 mg, 25%) as a pink solid. |
With bromine; sodium acetate | ||
With bromine; sodium acetate | ||
With bromine; sodium acetate; acetic acid at 20℃; for 12h; | ||
With bromine; sodium acetate; acetic acid In water | ||
With bromine In acetate buffer at 20℃; for 3h; | ||
With bromine at 20℃; for 3h; aq. acetate buffer; | ||
With bromine; acetic acid In 1,4-dioxane; water at 20℃; for 12h; Inert atmosphere; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
88% | With pyridine at 100℃; for 24h; | |
62% | Stage #1: N,N'-bis(dimethylaminomethylene)hydrazine; 2'-deoxy-D-adenosine With pyridine; chloro-trimethyl-silane for 21h; Stage #2: With methanol for 6h; Heating; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
92% | In water at 30℃; for 12h; | |
83% | With sodium hydrogencarbonate In tetrahydrofuran at 20℃; for 96h; | |
77% | Stage #1: 2'-deoxy-D-adenosine In water at 20℃; for 0.25h; Stage #2: 2-chloroethanal With sodium hydroxide In water for 28h; |
70% | With sodium acetate at 20℃; for 70h; | |
70% | In water at 20 - 50℃; for 70h; Sodium acetate buffer; | 1 Example 1 3-(2-Deoxy-β-D-erythro-pentofuranosyl)-3H-imidazo[2,1-i]purine (N1,N6-Etheno-2'-deoxyadenosine (5)). 2'-Deoxyadenosine monohydrate (1) (5.0 g, 20 mmol) was dissolved in 1M aq. sodium acetate buffer (pH 4.5 - 5.0, 110 mL) by warming to 40 - 50°C. To the solution chloroacetaldehyde (50% aq. soln, 7.7 mol/L, 25 mL) was added, and the reaction mixture was stirred for 70 h at room temperature. The yellow solution was evaporated to dryness, and the residue was dissolved in MeOH and filtered to remove inorganic salt. After washing with MeOH the combined filtrate and washings were concentrated in vacuo at 40 - 50°C. The residue was applied to FC (silica gel 60H, column: 20 x 6 cm). Elution with CH2Cl2-MeOH (85:15) gave a main fraction from which upon evaporation of the solvent and subsequent crystallization from MeOH-EtOAc compd. 5 (3.86 g, 70%) was isolated as colorless crystals. M.p. 138-141°C. TLC (silica gel, EtOAc-MeOH, 3:1): Rf 0.4. UV (MeOH): λmax 275 (7300), 265 (7600), 258 (6600), 229 nm (35700). 1H-NMR ([D6]DMSO) δ 2.39 (m, 1H, Hα-C(2')); 2.70 (m, 1H, Hβ-C(2')); 3.57 (m, 1H, Ha-C(5')); 3.67 (m, 1H, Hb-C(5')); 3.88 (m, 1H, H-C(4'); 4.43 (m, 1H, H-C(3')); 4.99 (t, 1H, 3J(H,H) = 5.2 Hz, 5'-OH); 5.38 (d, 1H, 3J(H,H) = 3.8 Hz, 3'-OH); 6.47 (pt, 1H, 3J(H,H) = 6.2 Hz, H-C(1')); 7.55 (s, 1H, H-C(11); 8.07 (s,1H, H-C(10); 8.53 (s, 1H, H-C(2)); 9.29 (s, 1H, H-C(8)). |
With aq. buffer (pH=4.5) | ||
In aq. phosphate buffer at 100℃; for 0.25h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
88% | With triphenylphosphine; diethylazodicarboxylate In tetrahydrofuran for 1h; Ambient temperature; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
100% | With water-d2; triethylamine at 65℃; for 65h; | |
60% | With [(2)H6]acetone; caesium carbonate In N,N-dimethyl-formamide at 80℃; for 1h; | |
With water-d2 at 90℃; for 5h; |
With water-d2 at 100℃; for 6h; | ||
With water-d2; triethylamine |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
75% | With potassium fluoride In N,N-dimethyl-formamide at 25℃; for 0.5h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
77% | With Enterobacter gergoviae CECT 875 in agarose In phosphate buffer at 60℃; for 1h; Enzymatic reaction; | |
67% | With Citrobacter koseri In aq. phosphate buffer at 60℃; for 1h; Microbiological reaction; | |
With aeromonas hydrophila CECT 4221 at 60℃; for 4h; aq. phosphate buffer; Enzymatic reaction; |
With Bacillus psychrosaccharolyticus CECT 4074 nucleoside 2'-deoxyribosyltransferase In aq. buffer at 40℃; for 0.0833333h; Enzymatic reaction; | N-Deoxyribosyltransferase Assay for Soluble BpNDT General procedure: The standard activity assay was performed by incubating 5 μL of cell extract or 0.40 μg of pure enzyme with 10 mM deoxyuridine and 10 mM adenine in 50 mM HEPES buffer, pH 8.0 in a final volume of 40 μL. The reaction mixture was incubating at 40 °C, 30 r.p.m., for 5 min. Then, activity was stopped by addition of 40 μL of cold methanol in ice-bath and heating for 5 min at 95 °C as described for others NDTs [9]. After centrifugation at 9000 ×g for 2 min, samples were half-diluted with water and the nucleoside production was measured at 254 nm by HPLC (Agilent 1100 series) with an ACE 5 μm C18-PFP column 250 mm × 46 mm (Advanced Chromatography Technologies) equilibrated with 100% trimethyl ammonium acetate at a flow rate of 1 mL/min. Elution was carried out by a discontinuous gradient: 0-10 min, 100% to 90% trimethyl ammonium acetate and 0% to 10% acetonitrile, and 10-20 min, 90% to 100% trimethyl ammonium acetate and 10% to 0% acetonitrile. Enzymatic synthesis of natural nucleosides was carried out at standard conditions described above using 10 mM of different 2'-deoxyribonucleosides and bases. Retention times for the reference natural compounds were as follows: uracil (Ura): 5.41 min; 2'-deoxyuridine (dUrd): 9.16 min; adenine (Ade): 10.14 min; 2'-deoxyadenosine (dAdo): 15.50 min; hypoxanthine (Hyp): 7.34 min; 2'-deoxyinosine (dIno): 10.95 min; thymine (Thy): 9.13 min; thymidine (Thd): 13.25; uric acid (UAc): 3.50 min. All determinations were carried out by triplicate and the maximum error was below 5%. In such conditions, one international activity unit (IU) was defined as the amount of enzyme producing 1 μmol/min of 2'-deoxyadenosine under the assay conditions. | |
With purine nucleoside phosphorylase; thymidine phosphorylase; phosphoric acid In aq. phosphate buffer at 37℃; for 24h; Enzymatic reaction; | 10 (Reference Examples 1 to 28) General procedure: In a 1.5 mL tube, 50 μL (pH 6.8) of a phosphate buffer solution,Raw materials Nucleoside compound 50 mM (each manufactured by Sigma),The target nucleoside compound base (see Table 2) 50 mM,Nucleoside phosphorylase (thymidine phosphorylase,Purine nucleoside phosphorylase, each manufactured by Sigma), 950 μL of waterWas obtained. The final concentration of phosphoric acid and the amount of enzyme are listed in Table 2.The mixture was allowed to react in a warm water bath at 37 ° C. for 24 hours,A small amount of the mixed solution after the reaction was separated and measured by HPLC,The amount of target nucleoside compound produced was confirmed.Table 2 shows the compound used in the reaction,And raw material nucleoside compound(Mol%) of the nucleoside compound to be produced. | |
With silica immobilized uridine phosphorylase from Clostridium perfringens and purine nucleoside phosphorylase from Aeromonas hydrophila In methanol; aq. phosphate buffer at 37℃; Flow reactor; Enzymatic reaction; | ||
With Clostridium perfringens uridine phosphorylase; Aeromonas hydrophila purine nucleosidephosphorylase co-immobilized on glyoxyl-agarose In aq. phosphate buffer at 28℃; Flow reactor; Green chemistry; Enzymatic reaction; | 3.9. General Procedure for the Flow Transglycosylation Reaction General procedure: A solution of the sugar donor and the sugar acceptor was prepared in 50mMphosphate buer pH7.5. In the case of hypoxanthine (6), in order to dissolve it, the suspension was sonicated (3 10 min).The temperature was set at 28 C. The column packed with immobilized CpUP and AhPNP (0.68 g,0.68 mL) was washed with 50 mM phosphate buer pH 7.5 at 0.2 mL min1 for 10 min at atmosphericpressure. The substrate solution (2.0 mL) was flowed through the bioreactor. Residence times andconcentrations were varied as reported in Table 1. The reaction outcome was monitored by HPLC. Asample of the exiting flow stream (200 L) was diluted with a mixture of H2O/MeOH (9:1), in order toobtain a sample concentration of 0.1 mM, and was used for the analysis. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
87% | With nucleoside deoxyribosyltransferase-II; sodium citrate at 40℃; for 20h; Enzymatic reaction; | |
With purine nucleoside phosphorylase; thymidine phosphorylase; phosphoric acid In aq. phosphate buffer at 37℃; for 24h; Enzymatic reaction; | 7 (Reference Examples 1 to 28) General procedure: In a 1.5 mL tube, 50 μL (pH 6.8) of a phosphate buffer solution,Raw materials Nucleoside compound 50 mM (each manufactured by Sigma),The target nucleoside compound base (see Table 2) 50 mM,Nucleoside phosphorylase (thymidine phosphorylase,Purine nucleoside phosphorylase, each manufactured by Sigma), 950 μL of waterWas obtained. The final concentration of phosphoric acid and the amount of enzyme are listed in Table 2.The mixture was allowed to react in a warm water bath at 37 ° C. for 24 hours,A small amount of the mixed solution after the reaction was separated and measured by HPLC,The amount of target nucleoside compound produced was confirmed.Table 2 shows the compound used in the reaction,And raw material nucleoside compound(Mol%) of the nucleoside compound to be produced. | |
With recobinant purine nucleoside phosphorylase from Escherichia coli; recombinant thymidine phosphorylase from Escherichia coli In aq. phosphate buffer for 8h; Heating; Enzymatic reaction; |
With Clostridium perfringens uridine phosphorylase; Aeromonas hydrophila purine nucleosidephosphorylase co-immobilized on glyoxyl-agarose In aq. phosphate buffer at 28℃; Flow reactor; Green chemistry; Enzymatic reaction; | 3.9. General Procedure for the Flow Transglycosylation Reaction General procedure: A solution of the sugar donor and the sugar acceptor was prepared in 50mMphosphate buer pH7.5. In the case of hypoxanthine (6), in order to dissolve it, the suspension was sonicated (3 10 min).The temperature was set at 28 C. The column packed with immobilized CpUP and AhPNP (0.68 g,0.68 mL) was washed with 50 mM phosphate buer pH 7.5 at 0.2 mL min1 for 10 min at atmosphericpressure. The substrate solution (2.0 mL) was flowed through the bioreactor. Residence times andconcentrations were varied as reported in Table 1. The reaction outcome was monitored by HPLC. Asample of the exiting flow stream (200 L) was diluted with a mixture of H2O/MeOH (9:1), in order toobtain a sample concentration of 0.1 mM, and was used for the analysis. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
84% | With potassium phosphate; sodium iodide; N,N`-dimethylethylenediamine In dimethyl sulfoxide at 110℃; for 3.5h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
80% | With potassium phosphate; sodium iodide; N,N`-dimethylethylenediamine In dimethyl sulfoxide at 110℃; for 3.5h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
82% | With potassium phosphate; sodium iodide; N,N`-dimethylethylenediamine In dimethyl sulfoxide at 110℃; for 3h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
81% | With hydrogen; water-d2 at 160℃; for 24h; | |
81% | With water-d2 at 110℃; for 24h; | |
With deuterium In water-d2 at 55℃; for 36h; Glovebox; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
87% | With tetraethylammonium fluoride; 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene In dimethyl sulfoxide at 90℃; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
73% | With sodium methylate In methanol at 20 - 45℃; for 1.16667h; | 1.2 EXAMPLE 1 ;[0037] 6-Amino-9-(2-deoxy-?-D-erythropentofuranosvl)purine (2?-Deoxyadenosine)10a [0038] 2. To a solution of 6-heptanoylamido-9-pentofuranosyl purine (product of 1a; 5.99 g; 10 mmol) in anhydrous methanol (50 ml) at 45 C. was added 25% CH3ONaCH3OH (1.6 ml; 7 mmol) all at once and the solution was held at 45 C. with stirring for 10 minutes followed by stirring at room temperature for 1 h. The solution was cooled with stirring (ice-bath) for 1 h. The separated solid was collected by filtration and washed with methanol (1?10 ml). Finally the solid was crystallized from water to yield 1.83 g (73%) of the product 10a; m.p. 188-190 C. [lit-m.p. 187-189 C., and all other physiochemical properties of the titled 2-deoxy adenosine product are identical with 2-deoxy adenosine reported in the literature]. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
91.2% | With tetrabutyl ammonium fluoride In tetrahydrofuran at 20℃; for 5h; | 4 Example 4; 2'-Deoxyadenosine; Procedure D To a solution of 2'-deoxy-3',5'-O-TIPDS-adenosine, (8A) (2.557 g, 5.18 mmol) in THF (15 mL) is added TBAF (10.4 mL, 1M in THF). The solution is stirred at room temperature for 5 hours. The solution is concentrated in vacuo and the residue is partitioned between water (100 mL) and dichloromethane (100 mL). The layers are separated and the aqueous layer is washed with dichloromethane (2×50 mL). The aqueous phase is concentrated in vacuo, and the residue is purified on a column of Dowex 1-X2 (OH-) resin. The product is eluted with water, collected, evaporated and crystallized in ethanol to give 2'-deoxyadenosine (10A) (1.187 g, 91.2%). Melting point 190-19°2 C. 1H NMR (DMSO) d 2.27 (ddd, J=13.2, 6.1, 2.8 Hz, 1, H2'), 2.75 (ddd, J=13.2, 7.8, 5.8 Hz, 1, H2), 3.60 (m,2, H5',5), 3.90 (dd, J=6.6, 4.0 Hz, 1, H3'), 4.43 (m, 1, H4'), 5.27 (t, J=5.9 Hz, 1, OH5'), 5.34 (d, J=3.9 Hz, 1, OH3'), 6.37 (dd, J=6.1, 7.8 Hz, 1, H1'), 7.35 (br s, 2, NH2), 8.15 & 8.36 (s, s, 2, H2,8). MS (FAB) m/z 252.1090 (MH+[C10H14N5O3]=252.1097. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
56% | With pyridine; di-isopropyl azodicarboxylate; triphenylphosphine at 20℃; for 0.583333h; | 1 5'-0-[4-bis(2-chloroethyl)-p-aminobenzenebutyryl]-2'-deoxyadenosine (dA - CLB). In the 50 ml flask 377 mg (1.5 mmol) of 2'-deoxyadenosine, 456 mg (1.5 mmol) of 4-bis(2- chloroethyl) -p-aminobenzenebutanoic acid and 10 ml of dry pyridine were placed. The solvent was evaporated to remove water from the sample. This action was repeated with a new portion of pyridine - 10 ml. Then, 12 ml of pyridine was added and stirred at room temperature for about 5 min and triphenylphosphine (525 mg, 2 mmol) and diisopropyl azodicarboxylate (405 mg, 2 mmol) were added portionwise and the sample was stirred for another 30 min. After that, the sample was evaporated to an oil. To remove the remaining pyridine, the sample was thrice evaporated with toluene (3 x 15 ml). The residue was applied onto a silica gel column (3 x 25 cm, silica gel 60, Merck) and chromatographed with methylene chloride (400 ml) and, then, with the mixture of methylene chloride - methanol (95: 5). The fractions containing product were evaporized to a dry foam. 452 mg of the compound was obtained. Yield 56%. TLC: Rf (MeOH/CHCl3) : 0.44. 1H NMR (D6Me2SO, 5(ppm)): 1.74-2.80 (2m, H-2' and H-2" and-CH2-CH2-CH2-), 3.68 (bs, N-CH2-CH2-), 4.00 (m, H-4'), 4.18 and 4.25 (2m, H-5' and H-5"), 4.47 (m, H-3'), 5.50. (bs, OH-3'), 6.36 (t, H-1'), 6.98 and 6.64 (2d, H-phenyl), 7.29 (s, NH2), 8.15 and 8.30 (2s, H-2 and H-8). ESI - TOF mass enumerated for C25H32Cl2N6O4 (M+Na+) 559.1598. Found: 559.1582. Elemental analysis: calculated for C25H32Cl2N6O4 (537.45) : C, 53.64; H, 5.63; N, 15.64. Found: C 53.37; H, 5.55; N, 15.54. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
99% | With sodium hydroxide In water | 50 Preparation of 2'-deoxyadenosine Example 50 Preparation of 2'-deoxyadenosine To 20 g of purified water were added 3.22 g of 2-deoxyribose-1-phosphate di(monocyclohexylammonium) salt prepared in Example 24 (7.72 mmol), 1.01 g of adenine (7.47 mmol) and 0.67 g of magnesium hydroxide (11.48 mmol). The reaction mixture was adjusted to pH 8.6 with a 20% aqueous solution of sodium hydroxide. To the mixture was added 0.1 mL of the above enzyme solution (0.1 mL), and the mixture was reacted with stirring at 50° C. for 3 hours. HPLC analysis for the reaction mixture after 8 hours indicated that the desired 2'-deoxyadenosine was provided with a reaction yield of 99%. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
99% | With tris-(trimethylsilyl)silane; 2-hydroxyethanethiol In water at 100℃; for 4h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
82% | With caesium carbonate; N,N`-dimethylethylenediamine In dimethyl sulfoxide at 110℃; for 8h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
79% | With caesium carbonate; N,N`-dimethylethylenediamine In dimethyl sulfoxide at 110℃; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
84% | With copper(l) iodide; caesium carbonate In N,N-dimethyl-formamide at 80℃; for 13h; | |
65% | With piperidine; copper(l) iodide; palladium diacetate; caesium carbonate In N,N-dimethyl-formamide at 80℃; for 15h; Inert atmosphere; | |
52% | With copper(l) iodide; caesium carbonate In N,N-dimethyl-formamide at 60℃; for 15h; Inert atmosphere; Schlenk technique; | General procedure for C8-arylation of 2'-deoxyadenosine 10 at 60 °C 2'-Deoxyadenosine (251 mg, 1.0 mmol, 1.0 equiv), CuI (571 mg, 3.0 mmol, 3 equiv), caesium carbonate (815 mg, 2.5 mmol, 2.5 equiv) and Pd catalyst (mol %) were added to a Schlenk under a N2 atmosphere. DMF (5.3 mL) and the aryl iodide (2.0 mmol, 2.0 equiv) were added and the reaction was stirred at 60 °C for either 24 or 48 h. The reaction was then cooled to room temperature, and HCl (5.3 mL, 1 M) was added to acidify the crude mixture. The pH was tested, and NaOH (1 M) was added until the pH reached 6.5. The reaction mixture was then extracted with EtOAc/iPrOH (5*25 mL, 9:1 v/v), dried over MgSO4 and the solvent removed in vacuo. The crude product was redissolved in MeOH/CH2Cl2 (1:1 v/v) and absorbed onto silica. The product was then purified by column chromatography on silica gel, eluting with MeOH/CH2Cl2 (2:98→1:9 v/v). The solvent was removed in vacuo to yield the pure product. The characterisation data for compound 12 (and 14, 16 and 18) has previously been reported by us. 32 |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
71% | With piperidine; copper(l) iodide; palladium diacetate; caesium carbonate In N,N-dimethyl-formamide at 80℃; for 15h; Inert atmosphere; | |
53% | With copper(l) iodide; caesium carbonate In N,N-dimethyl-formamide at 60℃; for 15h; Inert atmosphere; Schlenk technique; | General procedure for C8-arylation of 2'-deoxyadenosine 10 at 60 °C 2'-Deoxyadenosine (251 mg, 1.0 mmol, 1.0 equiv), CuI (571 mg, 3.0 mmol, 3 equiv), caesium carbonate (815 mg, 2.5 mmol, 2.5 equiv) and Pd catalyst (mol %) were added to a Schlenk under a N2 atmosphere. DMF (5.3 mL) and the aryl iodide (2.0 mmol, 2.0 equiv) were added and the reaction was stirred at 60 °C for either 24 or 48 h. The reaction was then cooled to room temperature, and HCl (5.3 mL, 1 M) was added to acidify the crude mixture. The pH was tested, and NaOH (1 M) was added until the pH reached 6.5. The reaction mixture was then extracted with EtOAc/iPrOH (5*25 mL, 9:1 v/v), dried over MgSO4 and the solvent removed in vacuo. The crude product was redissolved in MeOH/CH2Cl2 (1:1 v/v) and absorbed onto silica. The product was then purified by column chromatography on silica gel, eluting with MeOH/CH2Cl2 (2:98→1:9 v/v). The solvent was removed in vacuo to yield the pure product. The characterisation data for compound 12 (and 14, 16 and 18) has previously been reported by us. 32 |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
85% | With piperidine; copper(l) iodide; palladium diacetate; caesium carbonate In N,N-dimethyl-formamide at 80℃; for 15h; Inert atmosphere; | |
38% | With copper(l) iodide; caesium carbonate In N,N-dimethyl-formamide at 60℃; for 15h; Inert atmosphere; Schlenk technique; | General procedure for C8-arylation of 2'-deoxyadenosine 10 at 60 °C 2'-Deoxyadenosine (251 mg, 1.0 mmol, 1.0 equiv), CuI (571 mg, 3.0 mmol, 3 equiv), caesium carbonate (815 mg, 2.5 mmol, 2.5 equiv) and Pd catalyst (mol %) were added to a Schlenk under a N2 atmosphere. DMF (5.3 mL) and the aryl iodide (2.0 mmol, 2.0 equiv) were added and the reaction was stirred at 60 °C for either 24 or 48 h. The reaction was then cooled to room temperature, and HCl (5.3 mL, 1 M) was added to acidify the crude mixture. The pH was tested, and NaOH (1 M) was added until the pH reached 6.5. The reaction mixture was then extracted with EtOAc/iPrOH (5*25 mL, 9:1 v/v), dried over MgSO4 and the solvent removed in vacuo. The crude product was redissolved in MeOH/CH2Cl2 (1:1 v/v) and absorbed onto silica. The product was then purified by column chromatography on silica gel, eluting with MeOH/CH2Cl2 (2:98→1:9 v/v). The solvent was removed in vacuo to yield the pure product. The characterisation data for compound 12 (and 14, 16 and 18) has previously been reported by us. 32 |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
75% | With piperidine; copper(l) iodide; palladium diacetate; caesium carbonate In N,N-dimethyl-formamide at 80℃; for 15h; Inert atmosphere; | |
55% | With copper(l) iodide; caesium carbonate In N,N-dimethyl-formamide at 60℃; for 15h; Inert atmosphere; Schlenk technique; | General procedure for C8-arylation of 2'-deoxyadenosine 10 at 60 °C 2'-Deoxyadenosine (251 mg, 1.0 mmol, 1.0 equiv), CuI (571 mg, 3.0 mmol, 3 equiv), caesium carbonate (815 mg, 2.5 mmol, 2.5 equiv) and Pd catalyst (mol %) were added to a Schlenk under a N2 atmosphere. DMF (5.3 mL) and the aryl iodide (2.0 mmol, 2.0 equiv) were added and the reaction was stirred at 60 °C for either 24 or 48 h. The reaction was then cooled to room temperature, and HCl (5.3 mL, 1 M) was added to acidify the crude mixture. The pH was tested, and NaOH (1 M) was added until the pH reached 6.5. The reaction mixture was then extracted with EtOAc/iPrOH (5*25 mL, 9:1 v/v), dried over MgSO4 and the solvent removed in vacuo. The crude product was redissolved in MeOH/CH2Cl2 (1:1 v/v) and absorbed onto silica. The product was then purified by column chromatography on silica gel, eluting with MeOH/CH2Cl2 (2:98→1:9 v/v). The solvent was removed in vacuo to yield the pure product. The characterisation data for compound 12 (and 14, 16 and 18) has previously been reported by us. 32 |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
91% | Stage #1: 2'-deoxy-D-adenosine With pyridine; diphenyl hydrogen phosphate at 20℃; for 0.25h; Inert atmosphere; Stage #2: triethylamine In water at 20℃; for 0.25h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
97% | With piperidine; copper(l) iodide; palladium diacetate; caesium carbonate In N,N-dimethyl-formamide at 80℃; for 15h; Sealed vessel; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
87% | With piperidine; copper(l) iodide; palladium diacetate; caesium carbonate In N,N-dimethyl-formamide at 80℃; for 15h; Sealed vessel; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
63% | With sodium hydrogencarbonate; sodium chloride In methanol; dichloromethane | 2 2'-deoxy-5'-toluenesulphonyladenosine Preparation 2 2'-deoxy-5'-toluenesulphonyladenosine 2 g of 2'-deoxyadenosine (8 mmol) in a 0.1 M solution is introduced into anhydrous pyridine in a two-necked flask under an anhydrous nitrogen atmosphere. The solution is then cooled down to 0° C. and 3.793 g of paratoluene sulphonic acid chloride (2.5 equivalents, 20 mmol) are added by small portions. The reaction medium is left to return to ambient temperature, then stirred for 10 hours. The reaction is then stopped by the addition of 10 mL of methanol, stirring is maintained for 30 min. 50 mL of CH2Cl2 is added to the mixture then it is washed successively with 20 mL of a 5% solution of NaHCO3, 20 mL of a saturated solution of NaCl and 20 mL of a 5% solution of NaHCO3. The solvent is eliminated under reduced pressure. The expected compound is obtained pure by recrystallization from methanol. 2.1 g of a white product is isolated in this way. Rf: 0.37 (AcOEt/MeOH 9/1) The yield is 63%. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With Crotalus adamanteus venom phosphodiesterase I; bovine intestinal mucosa alkaline phosphatase; water; magnesium chloride; at 37℃; for 18h;pH 7.0;aq. phosphate buffer; Enzymatic reaction; | General procedure: Column containing solid support with the synthesized oligonucleotide was attached to a syringe containing 2 mL of 0.4 M solution of DBU in anhydr CH3CN. Approx. 0.7 mL of the solution was pushed into the column, replaced by a new portion after 5 min and another one after next 5 min. After total time of 15 min the support was washed with dry CH3CN (10 mL) and dried in vacuo. The dried support was placed into a vial, 1 mL of approx. 22% methanolic ammonia was added and the vial closed tightly. After 3 h at rt the solid was filtered off, washed with methanol and water and the filtrates were evaporated. The residue was dissolved in 0.1 m ammonium acetate (1 mL) and passed through a NAP 25 column. The column was washed with the same solution and 6 fractions of 1.4 mL were collected and checked by UV. The oligomer was present mainly in the fractions 3 and 4, with some residue in 5th fraction. Combined fractions were evaporated, dissolved in H2O/acetonitrile, 95/5, v/v (1 mL) and purified by HPLC (two 500 mul injections, Waters XBridge OST C18 Column, 2.5 mum,10 × 50 mm, phase A = 0.1 M TEAA, B = 0.1 M TEAA/Acetonitrile, 50/50, v/v, flow rate 1 ml/min, T = 40 C, gradient 17-20%B in 10 min, then to 50%B in 5 min. Combined fractions were concentrated to approx. 0.5 mL and desalted by passage through HPLC column. Yields of the oligomers BS3-BS6 see Table 1. The oligomerswere verified by enzymatic digestion, results see Table 3. Enzymatic digestion conditions: 0.2 OD of oligonucleotide in 150 muL of buffer (10 mM KH2PO4, 10 mM MgCl2, pH 7) was digested with alkaline phosphatase bovine intestinal mucosa (27 DEA units, Sigma-Aldrich, BioUltra) and phosphodiesterase I from Crotalus adamanteus venom (0.0055 units, Sigma-Aldrich, Purified) for 18 h at 37 C. The enzyme caused partial deamination of dA to dI (confirmed in model experiment). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With Crotalus adamanteus venom phosphodiesterase I; bovine intestinal mucosa alkaline phosphatase; water; magnesium chloride; at 37℃; for 18h;pH 7.0;aq. phosphate buffer; Enzymatic reaction; | General procedure: Column containing solid support with the synthesized oligonucleotide was attached to a syringe containing 2 mL of 0.4 M solution of DBU in anhydr CH3CN. Approx. 0.7 mL of the solution was pushed into the column, replaced by a new portion after 5 min and another one after next 5 min. After total time of 15 min the support was washed with dry CH3CN (10 mL) and dried in vacuo. The dried support was placed into a vial, 1 mL of approx. 22% methanolic ammonia was added and the vial closed tightly. After 3 h at rt the solid was filtered off, washed with methanol and water and the filtrates were evaporated. The residue was dissolved in 0.1 m ammonium acetate (1 mL) and passed through a NAP 25 column. The column was washed with the same solution and 6 fractions of 1.4 mL were collected and checked by UV. The oligomer was present mainly in the fractions 3 and 4, with some residue in 5th fraction. Combined fractions were evaporated, dissolved in H2O/acetonitrile, 95/5, v/v (1 mL) and purified by HPLC (two 500 mul injections, Waters XBridge OST C18 Column, 2.5 mum,10 × 50 mm, phase A = 0.1 M TEAA, B = 0.1 M TEAA/Acetonitrile, 50/50, v/v, flow rate 1 ml/min, T = 40 C, gradient 17-20%B in 10 min, then to 50%B in 5 min. Combined fractions were concentrated to approx. 0.5 mL and desalted by passage through HPLC column. Yields of the oligomers BS3-BS6 see Table 1. The oligomerswere verified by enzymatic digestion, results see Table 3. Enzymatic digestion conditions: 0.2 OD of oligonucleotide in 150 muL of buffer (10 mM KH2PO4, 10 mM MgCl2, pH 7) was digested with alkaline phosphatase bovine intestinal mucosa (27 DEA units, Sigma-Aldrich, BioUltra) and phosphodiesterase I from Crotalus adamanteus venom (0.0055 units, Sigma-Aldrich, Purified) for 18 h at 37 C. The enzyme caused partial deamination of dA to dI (confirmed in model experiment). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With Crotalus adamanteus venom phosphodiesterase I; bovine intestinal mucosa alkaline phosphatase; water; magnesium chloride; at 37℃; for 18h;pH 7.0;aq. phosphate buffer; Enzymatic reaction; | General procedure: Column containing solid support with the synthesized oligonucleotide was attached to a syringe containing 2 mL of 0.4 M solution of DBU in anhydr CH3CN. Approx. 0.7 mL of the solution was pushed into the column, replaced by a new portion after 5 min and another one after next 5 min. After total time of 15 min the support was washed with dry CH3CN (10 mL) and dried in vacuo. The dried support was placed into a vial, 1 mL of approx. 22% methanolic ammonia was added and the vial closed tightly. After 3 h at rt the solid was filtered off, washed with methanol and water and the filtrates were evaporated. The residue was dissolved in 0.1 m ammonium acetate (1 mL) and passed through a NAP 25 column. The column was washed with the same solution and 6 fractions of 1.4 mL were collected and checked by UV. The oligomer was present mainly in the fractions 3 and 4, with some residue in 5th fraction. Combined fractions were evaporated, dissolved in H2O/acetonitrile, 95/5, v/v (1 mL) and purified by HPLC (two 500 mul injections, Waters XBridge OST C18 Column, 2.5 mum,10 × 50 mm, phase A = 0.1 M TEAA, B = 0.1 M TEAA/Acetonitrile, 50/50, v/v, flow rate 1 ml/min, T = 40 C, gradient 17-20%B in 10 min, then to 50%B in 5 min. Combined fractions were concentrated to approx. 0.5 mL and desalted by passage through HPLC column. Yields of the oligomers BS3-BS6 see Table 1. The oligomerswere verified by enzymatic digestion, results see Table 3. Enzymatic digestion conditions: 0.2 OD of oligonucleotide in 150 muL of buffer (10 mM KH2PO4, 10 mM MgCl2, pH 7) was digested with alkaline phosphatase bovine intestinal mucosa (27 DEA units, Sigma-Aldrich, BioUltra) and phosphodiesterase I from Crotalus adamanteus venom (0.0055 units, Sigma-Aldrich, Purified) for 18 h at 37 C. The enzyme caused partial deamination of dA to dI (confirmed in model experiment). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With Crotalus adamanteus venom phosphodiesterase I; bovine intestinal mucosa alkaline phosphatase; water; magnesium chloride; at 37℃; for 18h;pH 7.0;aq. phosphate buffer; Enzymatic reaction; | General procedure: Column containing solid support with the synthesized oligonucleotide was attached to a syringe containing 2 mL of 0.4 M solution of DBU in anhydr CH3CN. Approx. 0.7 mL of the solution was pushed into the column, replaced by a new portion after 5 min and another one after next 5 min. After total time of 15 min the support was washed with dry CH3CN (10 mL) and dried in vacuo. The dried support was placed into a vial, 1 mL of approx. 22% methanolic ammonia was added and the vial closed tightly. After 3 h at rt the solid was filtered off, washed with methanol and water and the filtrates were evaporated. The residue was dissolved in 0.1 m ammonium acetate (1 mL) and passed through a NAP 25 column. The column was washed with the same solution and 6 fractions of 1.4 mL were collected and checked by UV. The oligomer was present mainly in the fractions 3 and 4, with some residue in 5th fraction. Combined fractions were evaporated, dissolved in H2O/acetonitrile, 95/5, v/v (1 mL) and purified by HPLC (two 500 mul injections, Waters XBridge OST C18 Column, 2.5 mum,10 × 50 mm, phase A = 0.1 M TEAA, B = 0.1 M TEAA/Acetonitrile, 50/50, v/v, flow rate 1 ml/min, T = 40 C, gradient 17-20%B in 10 min, then to 50%B in 5 min. Combined fractions were concentrated to approx. 0.5 mL and desalted by passage through HPLC column. Yields of the oligomers BS3-BS6 see Table 1. The oligomerswere verified by enzymatic digestion, results see Table 3. Enzymatic digestion conditions: 0.2 OD of oligonucleotide in 150 muL of buffer (10 mM KH2PO4, 10 mM MgCl2, pH 7) was digested with alkaline phosphatase bovine intestinal mucosa (27 DEA units, Sigma-Aldrich, BioUltra) and phosphodiesterase I from Crotalus adamanteus venom (0.0055 units, Sigma-Aldrich, Purified) for 18 h at 37 C. The enzyme caused partial deamination of dA to dI (confirmed in model experiment). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
95% | In pyridine at 65℃; for 4h; | |
93% | With pyridine at 80℃; for 4h; | 4.2. N,N-Dibenzoyl-3′,5′-dibenzoyl-2′-deoxyadenosine (5) Benzoyl chloride (6.29 g, 44.74 mmol) was added dropwise to a suspensionof 2′-deoxyadenosine (2.00 g, 7.99 mmol) in pyridine (20 mL) at 0 °C. Tocomplete the reaction, the mixture was stirred and heated to 80 °C for4 h. Then the solvent was removed in vacuo. The resulting residue wasdissolved in CH2Cl2 (100 mL) and washed with H2O (100 mL). The aqueouslayer was extracted with CH2Cl2 (3 × 50 mL). The combined organic layerswere washed with brine (100 mL), dried on anhydrous Na2SO4 and concentratedin vacuo. The resulting residue was recrystallized from EtOH togive 5 (3.84 g, 72% yield) as a white solid. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
62% | Stage #1: 2'-deoxy-D-adenosine With chloro-trimethyl-silane In pyridine at 20℃; for 0.5h; Stage #2: (4-tert-butylphenoxy)acetyl chloride In pyridine at 20℃; for 2h; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
86.7% | With lithium triethylborohydride In tetrahydrofuran at 0 - 5℃; for 3h; Inert atmosphere; | 2.2 (2) the the 2 [...] -O-P-toluene sulphonyl adenosine (III) synthesis of the 2 [...] -deoxy adenosine (IV) Weighed the 2 [...] -O-P-toluene sulphonyl adenosinergic 1.69g, water-free tetrahydrofuran 30 ml, the above-mentioned raw material in a 100 ml round-bottom flask, nitrogen protection, 0-5 °C slowly dripping 1mol/L triethylborane lithium hydride tetrahydrofuran solution of 25 ml, drop end continuing to stir 1h 2h, and then transfer to stir at room temperature 6-8h, reaction 6-8ml methanol-quenched reaction, first rotary evaporated to remove the tetrahydrofuran, then decompressing and evaporate dimethyl sulfoxide, finally recrystallized with ethanol to obtain white crystalline product 0.89g, yield of 86.7%. To measure the purity HPLC> 99.0%. |
84.6% | With lithium aluminium tetrahydride In tetrahydrofuran at 0 - 20℃; for 10h; Inert atmosphere; | Synthesis of 2'-deoxyadenosine (17) Under nitrogen atmosphere, 2'-O-p-toluenesulfonyladenosine16 (2.11 g, 5 mmol) and anhydrous tetrahydrofuran(THF, 35 mL) were placed in a 100 mL roundbottomflask. Lithium aluminum hydride in anhydrous THF(LiAlH4/THF, 1 M, 25 mL) was slowly dropped to thesolution and the resulting mixture was stirred at 0-5 C for4 h and was then continued to stir at room temperature for6 h. After reaction completion, the mixture was carefullyquenched with 10 mL of methanol, concentrated in vacuo,and recrystallization from ethanol to afford pure 17(1.06 g, 84.6%) as a white powder with the purity of 98.3%(HPLC). 1H NMR (400 MHz, DMSO-d6) d 8.34 (s, 1H,8-H), 8.13 (s, 1H, 2-H), 7.32 (s, 2H, -NH2), 6.35 (dd,J = 7.9, 6.1 Hz, 1H, 10-H), 5.31 (dd, J = 4.0, 1.3 Hz, 1H,30-OH), 5.25 (dd, J = 6.6, 4.8 Hz, 1H, 50-OH), 4.43-4.39(m, 1H, 30-H), 3.90-3.87 (m, 1H, 40-H), 3.65-3.60 (m, 1H,50-H), 3.55-3.49 (m, 1H, 50-H), 2.77-2.70 (m, 1H, 20-H),2.28-2.23 (m, 1H, 20-H). 13C NMR (126 MHz, DMSO) d156.56 (6-C), 152.84 (2-C), 149.34 (4-C), 140.03 (8-C),119.72 (5-C), 88.46 (40-C), 84.42 (10-C), 71.45 (30-C),62.37 (50-C), 39.44 (20-C). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
76% | With nitric acid In water at 50℃; for 1h; | Typical procedure for oxidative desulfuration reactionwith HNO3 General procedure: 1a(0.142 g, 0.5 mmol) was slowly added to a stirred solution ofHNO3(50%, 5 mL). The mixture was heated to 50°Candkeptat this temperature for 1 hour. The solvent was neutralized by1 mol/L NaOH and was concentratedin vacuo.Thesaltswerefiltered and washed with EtOH (5 mL). The mother liquor wasevaporated to dryness and was recrystallized from H2Otogive2aas a white solid (0.103 g, 82% yield). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With purine nucleoside phosphorylase; phosphoric acid; In aq. phosphate buffer; at 37℃; for 24h;pH 6.8;Enzymatic reaction; | General procedure: In a 1.5 mL tube, 50 muL (pH 6.8) of a phosphate buffer solution,Raw materials Nucleoside compound 50 mM (each manufactured by Sigma),The target nucleoside compound base (see Table 2) 50 mM,Nucleoside phosphorylase (thymidine phosphorylase,Purine nucleoside phosphorylase, each manufactured by Sigma), 950 muL of waterWas obtained. The final concentration of phosphoric acid and the amount of enzyme are listed in Table 2.The mixture was allowed to react in a warm water bath at 37 C. for 24 hours,A small amount of the mixed solution after the reaction was separated and measured by HPLC,The amount of target nucleoside compound produced was confirmed.Table 2 shows the compound used in the reaction,And raw material nucleoside compound(Mol%) of the nucleoside compound to be produced. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
79% | With manganese(IV) oxide; C17H20N4O9P(1-)*Na(1+); oxygen In water; acetonitrile at 20℃; for 7h; Irradiation; chemoselective reaction; | |
60% | With Selectfluor; riboflavin In water; acetonitrile for 3h; Inert atmosphere; UV-irradiation; | 2 Deoxyribonucleoside demethylation of N6-methyladenine by using vitamin B2 as a photosensitizer under 470nm wavelength blue light and Selectfluor: and then into the reaction tube added the N6-methyladenine deoxyribonucleoside (0.1mmol, 26.5mg), Selectfluor (0.22mmol, 1,78mg), Vitamin B2 (0.01mmol, 3.8 mg), under nitrogen protection added 2 ml of H20 / CH3CN (1/1) solution, 470nm wavelength of blue light, stirring 3 hours, add the appropriate amount of sodium bicarbonate to the reaction solution at pH 7, spin dry liquid, after column chromatography (CH2Cl2/MeOH=12/1) separation obtained adenine deoxyribonucleoside 15mg, yield is 60%. |
60% | With Selectfluor; riboflavin In water; acetonitrile at 37℃; for 3h; Inert atmosphere; Irradiation; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
80% | Stage #1: tert-butyldimethylsilyl chloride; 2'-deoxy-D-adenosine With 1H-imidazole In N,N-dimethyl-formamide at 20℃; Stage #2: di-<i>tert</i>-butyl dicarbonate With dmap In N,N-dimethyl-formamide at 20℃; | 1.1.1 Synthetic route 1 wherein the reaction conditions of step (i) are: compound 10 mmol 2.5 g Α.1 in tert-butyldimethylchlorosilane (TBSCl) 4.82 g 32 mmol of imidazole and 4.5 g 66 mmol of N, N-dimethylformamide (DMF) 30 mL stored under conditions of room temperature overnight, then the reaction solution in di-tert-butyl ester (Boc)2O) 20 mmol 4.36 g, 4-dimethylaminopyridine (DMAP) 10 mmol 1.22 g and N,N-dimethylformamide (DMF) 30 ml were added to the reaction mixture at room temperature overnight, concentrated in vacuo, and the residue was washed twice (each 50ml) with saturated ammonium chloride solution, using CH2Cl2. The aqueous layer was dried over sodium sulfate and the organic layer was combined, concentrated in vacuo and purified by silica gel column chromatography to give compound A. 25.6 g 8 mmol (80%); In the above synthetic step (i), the added TBSCl may be any of 30 ~ 40 mmol; the added (Boc)2O can be any value in the range of 10 ~ 30 mmol |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With disodium dihydrogen hypodiphosphate hexahydrate; hypophosphoric acid In water at 142.84℃; | To obtain (III) and (IV), several methods were tried. Directreaction of adenine (Ade) with H4P2O6 in the molar ratio 2:1 (by dissolving the reagents in water and optionally heating themixture to dissolve Ade and leaving it to cool very slowly)gave pure compound (III), as shown by X-ray powderdiffraction (Fig. S1 in the supporting information), but thequality of the crystals (very thin plates or needles) did notallow determination of the crystal structure. Then, crystallizationfrom a solution of 20-deoxyadenosine (dAdo; AlfaAesar) and hypodiphosphoric acid was carried out.Na2(H2P2O6)6H2O (100 mg, 0.318 mmol) was dissolved in aminimum quantity of water and passed through an ionexchange column (Dowex 50-H+). The eluate (21 ml ofH4P2O6 solution; c = 0.015 M) was divided into four parts. Tothe hypodiphosphoric acid obtained (5.25 ml, 0.080 mmol)was added dAdo (10 mg, 0.040 mmol). During the hydrolysisof the nucleoside, adenine (Ade) was released slowly into thesolution and large crystals of (III) were grown by slowevaporation of the solution at room temperature [m.p. 414-416 K (decomposition)]. A dAdo:H4P2O6 molar ratio of 1:2gave the crystals of highest quality (one of them was used forsingle-crystal structure determination), but the same crystalform (small plates) was also obtained by the reaction of dAdoand H4P2O6 in molar ratios of 1:3 and 2:1. Analogous reactions with other adenine nucleosides, i.e. adenosine (Ubichem) and20:30-isopropylideneadenosine (Fluka), were tried withoutsuccess. ESI-MS (H2O/CH3OH/HCOOH): m/z = 136.1 [Ade +H]+. No m/z = 252.1 [dAdo + H]+. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With disodium dihydrogen hypodiphosphate hexahydrate; hypophosphoric acid In water at 6.84℃; Inert atmosphere; | For the synthesis of (IV), Na2(H2P2O6)6H2O (300 mg,0.955 mmol) was dissolved in a minimum quantity of waterand passed through an ion-exchange column (Dowex 50-H+).To 5.25 ml of the resulting 0.022 M H4P2O6 solution (19.3 mg,0.119 mmol) was added dAdo (14.9 mg, 0.059 mmol). Thesolution was concentrated under a nitrogen stream and left tostand at room temperature for slow crystallization. Afterstarting the crystallization, the sample was maintained at280 K to give crystals of (IV) [m.p. 406 K (decomposition)]. Along with (IV), another (triclinic) polymorphic form wasobtained under the same conditions [m.p. 440 K (decomposition)];the crystal structure is not presented here. Compound(IV) was also obtained by the room-temperature concentrationof the reaction mixture under a stream of N2. ESI-MS(H2O/CH3OH/HCOOH): m/z = 136.1 [Ade + H]+. No m/z =252.1 [dAdo + H]+. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
75% | With 2,2,6,6-Tetramethyl-1-piperidinyloxy free radical; [bis(acetoxy)iodo]benzene; sodium hydrogencarbonate In water; acetonitrile at 0 - 20℃; regioselective reaction; | General procedure for TEMPO-mediated oxidation using PhI(OAc)2: General procedure: TEMPO (0.2 equiv per 1o-OH group) and bis(acetoxy)iodobenzene (3 equiv per 1o-OH group) were added to a stirred solution of sugar/nucleoside (0.1 - 0.5 mmol) and NaHCO3 (2 equiv per 1o -OH group) in a MeCN:H2O (1:1, 2 mL) at 0 oC; stirring was continued at the same temperature for 5 min. After that the resulting mixture was warmed to room temperature and stirred for 15 min to complete one cooling-warming cycle. Again, the temperature of the reaction mixture was lowered to 0 oC for 5 minutes and then warmed to room temperature for 15 minutes to complete the second warming-cooling cycle and so on until most of the starting material was consumed (by mass/TLC analysis). After completion the reaction mixture was diluted with H2O and washed with EtOAc (to remove TEMPO). Aqueous layer was concentrated under vacuum to afford the crude product which was further purified by silica gel flash chromatography/ion exchange resin to afford the pure acid product as sodium salt/triethyl ammonium salt. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
15% | Stage #1: Methylenediphosphonic acid; 2'-deoxy-D-adenosine With dicyclohexyl-carbodiimide In N,N-dimethyl-formamide at 20℃; Stage #2: triethylamine carbonate In water; N,N-dimethyl-formamide at 20℃; for 0.5h; | |
15% | Stage #1: Methylenediphosphonic acid; 2'-deoxy-D-adenosine With dicyclohexyl-carbodiimide In N,N-dimethyl-formamide at 20℃; Stage #2: triethylamine carbonate In N,N-dimethyl-formamide at 20℃; for 0.5h; Cooling; | 1 General procedure A for the synthesis of nucleotides General procedure: To a solution of DCC (3 eq.) and nucleoside in DMF (2 mL) methylene diphosphonic acid (1.5 eq.) was added at rt and the mixture was allowed to stir at rt for 6-24 h. Samples were withdrawn at 3 - 12 h interval for LC-MS to check the disappearance of nucleosides and to monitor the formation of the desired nucleotide. On the disappearance of a nucleoside, 10 mL of cold TEAC-solution was added. The mixture was stirred at rt for 30 min followed by filtration and lyophilization of the aqueous solution. The mixture of nucleotide and dinucleotide was separated by ion-exchange chromatography on Source 15Q. Fractions containing the product were pooled and evaporated to dryness. The compound was then purified by RP-HPLC using a gradient of 10 mM triethylammonium acetate buffer - CHbCN from 80:20 to 20:80 in 40 min, suitable fractions were pooled and lyophilized to obtain the final product as glassy solid |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
99% | In aq. buffer at 60℃; for 8h; | |
74.1% | With sodium hydroxide In aq. phosphate buffer at 50℃; for 8h; | 1.1 1. Preparation of N1-carboxymethyl-deoxyadenosine (Compound 1) pH=7.0, 0.1mol/L phosphate buffer solution 5mlPour into a 10 ml round bottom flask.1500 mg of iodoacetic acid was added to the round bottom flask.Then add deoxyadenosine 400mg,Micro-heat dissolution.Adjust the pH with a 5mol/L NaOH solution.Let pH = 7.0.At this time, a large amount of inorganic salt white flocculent solid precipitated in the reaction liquid.Continue heating to 50 ° C,The solid disappears.Water bath, reflux reaction,The temperature is set to 50 ° C,Reaction 8h.After the reaction,The solution turned from orange to colorless to pink.The pH of the solution was adjusted to pH = 3 using 5 mol/L HCl. The reaction solution is added to a pre-cooled (-5 ° C) acetone solution,Precipitating solids,filter,After drying, the product was obtained 340 mg.The yield was 74.1%. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
23% | With dmap; triethylamine; dicyclohexyl-carbodiimide; In 1,4-dioxane; at 20℃; for 16h; | To (2R,35',5R)-5-(6-amino-9H-purin-9-yl)-2-(hydroxymethyl)tetrahydrofuran-3-ol (A-8) (1 g, 3.984 mmol) in 1,4-dioxane (20 mL, 20 vol) at rt was added <strong>[638-53-9]<strong>[638-53-9]tridecanoic</strong> acid</strong> (2.6 g, 11.95 mmol), TEA (2.8 mL, 19.9 mmol), DCC (2.5 g, 11.95 mmol) and DMAP (49 mg, 0.398 mmol. The reaction mixture was stirred at rt for 16 h. The solvent was then evaporated, and the residue was taken in water (100 mL) and extracted with ethyl acetate (4 x 50 mL). The combined organic layer was washed with water (50 mL), brine (50 mL), dried over anhydrous Na2S04; filtered, and 83 concentrated under reduced pressure. The residue was purified by silica gel chromatography (100- 200 mesh) and prep HPLC to afford (2R,3^,5R)-5-(6-amino-9H-purin-9-yl)-2- ((tridecanoyloxy)methyl)tetrahydrofuran-3-yl tridecanoate (Compound 5) (600 mg, 23%) as a white solid. MS (ESI) m/z 644.5 [M+H]+; 1H MR (400 MHz, DMSO-i) delta 8.32 (s, 1H), 8.14 (s, 1H), 7.30 (br s, 2H), 6.36 (t, J= 6.4 Hz, 1H), 5.44-5.40 (m, 1H), 4.35-4.28 (m, 1H), 4.26-4.17 (m, 2H), 3.18-3.11 (m, 1H), 2.45-2.50 (m, 1H), 2.36 (t, J= 7.6 Hz, 2H), 2.30-2.26 (m, 2H), 1.57-1.46 (m, 4H), 1.35-1.15 (m, 36H), 0.84 (t, J= 5.2 Hz, 6H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
9% | Stage #1: didecyl N,N-diisopropylphosphoramidite; 2'-deoxy-D-adenosine With 1H-tetrazole In tetrahydrofuran; dimethyl sulfoxide at 0 - 20℃; for 12h; Stage #2: With tert.-butylhydroperoxide In tetrahydrofuran; decane; dimethyl sulfoxide at 0 - 20℃; for 4h; | 29 Synthesis of Compound 6 To a stirred solution of A-8 (7 g, 27.88 mmol) in THF/DMSO (1 : 1, 140 mL) were added lH-tetrazole (5.85 g, 83.64 mmol) followed by didecyl diisopropylphosphoramidite (A-10) (14.89 g, 33.46 mmol) at 0 °C. The reaction mixture was stirred at rt for 12 h and then 5M TBHP in decane (16.72 mL, 83.64 mmol) at 0 °C was added. The reaction mixture was stirred at rt for 4 h. The reaction was then quenched with saturated NaHS03 solution and extracted with EtOAc (2 x 150 mL). The combined organic layers were washed with saturated NaHS03 solution (2 x 100 mL), brine (2 x 100 mL), dried over Na2S04, filtered, and concentrated under reduced pressure. The residue was purified by silica gel chromatography to afford ((2R,3S,5R)-5-(6-amino-9H-purin-9- yl)-3-hydroxytetrahydrofuran-2-yl) methyl didecyl phosphate (A-9) (2 g, 9%) as a liquid. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
In aq. acetate buffer;pH 3.7;UV-irradiation; | General procedure: dA (10 mM) and NPRO (100 mM) dissolved in sodium acetate buffer(3 M, pH 3.7) was irradiated using 20-W black light bulbs (Panasonic,Japan) emitting radiation in the range 300-400 nm in a chamber keptat 4 C. Use of a 4-mm thick glass plate between the light source and thereaction solution excluded radiation of wavelengths<320 nm. TheUVA dose rate at 360 nm was measured using a black-ray UV intensitymeter (Ultraviolet Products, San Gabriel CA). Light intensity was8.30±0.95 W/m2 at the surface of the solution, namely 359±41 kJ/m2 for 12 h, if not stated otherwise. Irradiated samples were analyzedusing HPLC apparatus equipped with a photodiode array detector SPPM10Avp (Shimadzu, Kyoto). The column used was Inertsil ODS-3 (4.6mm × 250 mm) and the eluent comprised 20 mM triethylammoniumacetate with 2-30% methanol (pH 7.0). Irradiated samples were fractionatedby HPLC with a column comprising TSK-GEL ODS-80 Ts (21.5mm × 300 mm) and eluent consisting of 40 mM triethylammoniumacetate with 15% methanol (pH 7.0). Peak fractions were collected andre-chromatographed by HPLC with a column comprising TSK-GEL ODS-80 Ts (4.6 mm × 250 mm) and eluent consisting of 20 mM triethylammoniumacetate (pH 7.0) with 20% methanol. 1H NMR spectra ofsamples dissolved in dimethylsulfoxide-d6 were recorded on a UnityINOVA AS600 spectrometer (Varian Technologies Japan LTD., Tokyo)at 600 MHz. Chemical shifts were based on those of the solvent signals(deltaH 2.49; deltaC 39.8) and given in delta (ppm) from tetramethylsilane. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
12.1% | With diatomaceous earth In acetyl chloride; N,N-dimethyl-formamide at 20℃; for 1h; Inert atmosphere; | 1. 2) The second step is to synthesize N6-methyldeoxyadenosine (dm6A) (shown in formula 2) Under the protection of argon,18.62g methyl p-toluenesulfonate (0.1mol, 4eq)Dissolved in 60ml DMF,6.28g 2'-deoxyadenosine (0.025mol, 1eq) was added.The reaction solution was stirred overnight at room temperature.Add 20 g of diatomaceous earth and filter.Add 900ml of acetone to the filtrate,Stir at room temperature for 1h,Solids are produced, filter.The solid is washed with acetone,Vacuum drying.The obtained solid was dissolved in 150ml 2M NaOH,Stir at room temperature for 1 h.The reaction liquid was neutralized with 10% p-toluenesulfonic acid aqueous solution,Dry the spin column (SiO2, DCM: MeOH = 10: 1) to give a white solid 0.8g, 12.1% yield. 3)The third step is to obtain N6-methyldeoxyadenosine. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
74% | Stage #1: 2'-deoxy-D-adenosine With pyridine; chloro-trimethyl-silane at 25℃; for 2h; Stage #2: dibenzoyl peroxide In lithium hydroxide monohydrate at 60℃; for 9h; | 1 Procedure: Compound b (190g, 0.756mol, 1.0eq.) was dissolved in pyridine (1.9L), TMSCl (329g, 3.024mol, 4.00eq.) was added, and the reaction was performed at 25±5°C for 2 hours.Then Bz2O (dibenzoyl peroxide, 342g, 1.512mol, 2.0eq.) was added, the reaction solution was heated to 60±5°C and stirred for 8 hours, then water (400mL) was added and stirred for 1 hour.Subsequently, the reaction solution was directly concentrated to dryness, EA (ethyl acetate, 1.9 L) was added to reconstitute, and each time was washed with water (1 L) for a total of two washes.After washing, liquid separation was carried out, and the separated organic phase was dried with anhydrous sodium sulfate, and concentrated to dryness at 35±5°C.Get crude.The crude product was suspended and stirred with EtOH/EA (ethanol:ethyl acetate; 1.8L/0.2L) for 30 minutes, filtered, and dried in vacuo to obtain 200 g of compound c with HPLC purity of 98.5%, molar yield: 74%. |
Tags: 958-09-8 synthesis path| 958-09-8 SDS| 958-09-8 COA| 958-09-8 purity| 958-09-8 application| 958-09-8 NMR| 958-09-8 COA| 958-09-8 structure
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